Fig. 6

Pathway and process enrichment analysis. A Bar graph of enriched terms across input gene lists, colored by p values. The network of enriched terms: B colored by cluster ID, where nodes that share the same cluster ID are typically close to each other. Each term is represented by a circle node, where its size is proportional to the number of input genes fall into that term, and its color represents its cluster identity (i.e., nodes of the same color belong to the same cluster). Terms with a similarity score > 0.3 are linked by an edge (the thickness of the edge represents the similarity score). The network is visualized with Cytoscape with “force-directed” layout and with edge bundled for clarity. One term from each cluster is selected to have its term description shown as label. C The same enrichment network has its nodes colored by p value, as shown in the legend. The dark the color, the more statistically significant the node is (see legend for p value ranges). D protein–protein interaction network and MCODE components identified in the gene lists. MCODE algorithm was then applied to this network to identify neighborhoods where proteins are densely connected. Each MCODE network is assigned a unique color. GO enrichment analysis was applied to each MCODE network to assign “meanings” to the network component